Well, the CTD did stay after I removed Interstellar Fuel Switch but the frequency seemed less. I will try and reproduce the error per ibanix's post and update the bug tracker if applicable.
Thanks everyone for the recommendations and help on this.
Update: Before I attempted to reproduce the error I had a CTD in the SPH deleting a single Mk1 fuel fuselage without having any symmetry enabled. I will reload the game and try to reproduce the error.